You might want to run more than one Emacs with more than one Gnus at the same time. If you are using different .newsrc files (e.g., if you are using the two different Gnusae to read from two different servers), that is no problem whatsoever. You just do it.
The problem appears when you want to run two Gnusae that use the same .newsrc file.
To work around that problem some, we here at the Think-Tank at the Gnus Towers have come up with a new concept: Masters and slaves. (We have applied for a patent on this concept, and have taken out a copyright on those words. If you wish to use those words in conjunction with each other, you have to send $1 per usage instance to me. Usage of the patent (Master/Slave Relationships In Computer Applications) will be much more expensive, of course.)
Anyway, you start one Gnus up the normal way with M-x gnus (or however you do it). Each subsequent slave Gnusae should be started with M-x gnus-slave. These slaves won't save normal .newsrc files, but instead save slave files that contain information only on what groups have been read in the slave session. When a master Gnus starts, it will read (and delete) these slave files, incorporating all information from them. (The slave files will be read in the sequence they were created, so the latest changes will have precedence.)
Information from the slave files has, of course, precedence over the information in the normal (i.e., master) .newsrc file.
If the .newsrc* files have not been saved in the master when the slave starts, you may be prompted as to whether to read an auto-save file. If you answer “yes”, the unsaved changes to the master will be incorporated into the slave. If you answer “no”, the slave may see some messages as unread that have been read in the master.